IonTorrent SOP

Commands in mothur
1

Hi,
In the IonTorrent SOP’s 1st step, a single SFF file is used (mothur > sffinfo(sff=IonOct.sff)). However, in the downloaded example files, there is no “IonOct.sff”, instead there are 18 different SFF files (IonOct49.SFF, IonOct51.SFF, etc.).
What should I do?
Thanks,
Chen

2

That SOP was posted by Sukithar Rajan (http://www.mothur.org/wiki/User:Suki) who isn’t affiliated with the mothur project. I’d encourage you to reach out to them and see what’s up.

Pat

3

Hi Chenazulay,

Thanks for pointing this out. There are two options to proceed from here. Either you can process the 18 files separately, or combine these files and continue as as single file.

If you prefer to continue as a single file, you can run, commands separately until step 1.3 (shhh.flows) and then merge the files together. Use the merged files from step 1.3 to do the trim.seqs (step 1.4) and other downstream analysis.

OR

If you would like to start with a combined sff file, pls let me know, I might still could provide you a single sff file.

Thanks
Suki